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<h1>Lab Notes - August</h1>

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<h1>Biobrick Group</h1>
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<h1>Week5</h1>


<table id="notesheet" width="696" border="1" cellspacing="1"
	cellpadding="1">
	<tr>
		<td width="63">Day</td>
		<td width="620">Note</td>
	</tr>

	<tr>
		<td id="sheetleft">Aug.1st Monday</td>
		<td>
		<table id="intable" width="541" border="0" cellspacing="1"
			cellpadding="1">
			<tr>
			<td width="286">•Fusion PCR Vgb+YFP+tetR, NirB+RFP+tetR,</td>
			<td width="251">•PCR: NirB, Vgb</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.2nd Tuesday</td>
		<td>
		<table id="intable" width="607" border="0" cellspacing="1"
			cellpadding="1">
			<tr>
			<td width="124">•Cut: 13K+10I, 22M+10I</td>
			<td width="180">• Purify: 13K+10I, 22M+10I<br />
			• Ligation: Pvgb+22M+10I, Pnirb+13K+10I</td>
			<td width="154">• PCR backbones<br />
			• Electrophresis</td>
			<td width="136">• Gel excision and purification</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.3rd Wednesday</td>
		<td>
		<table width="611" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="304">• Make Phusion Buffer, 5×isothermel buffer</td>
				<td width="300">• colony PCR: 20H, 20J, 22B</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.4th Thursday</td>
		<td>
		<table width="618" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td>• Cut: 10I+22M, 10I+13; and purification</td>
				<td>• Ligation: Pvgb+22M+10I, Pnirb+13K+10I,<br />
				• colony PCR: 13K+10I</td>
				<td>• Culture: 20H, 20J, 22B, 1K, 1I,3C, 5E, 7C</td>
				<td>• Transform: 1G, 3A, 5A, 7A from the distribution plate</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.5th Friday</td>
		<td>
		<table width="612" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="188">• Check the plates. Contamination, or no
				positive colonies</td>
				<td width="121">• Miniprep: 5 backbones, 22B-1, 22B-3</td>
				<td width="197">• PCR: nirB from 13K+10I+nirB to firm the
				ligation. One positive result.</td>
				<td width="93">• Culture the positive colony.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.6th Saturday</td>
		<td>
		<table width="620" border="0" cellspacing="1" cellpadding="1">
			<tr>


			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.7th Sunday</td>
		<td>
		<table width="610" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="244">• Cut: 22M,13K with E &amp; S</td>
				<td width="164">• Culture the red colonies from plate of pSB1C3</td>
				<td width="192">• PCR: 5 backbones<br />
				• Cut the PCR products with P+E and run the gel to confirm.</td>
			</tr>
		</table>
		</td>
	</tr>

</table>

<h1>Week6</h1>
<table id="notesheet" width="693" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td width="76">Day</td>
		<td width="349">Note</td>
	</tr>

	<tr>
		<td id="sheetleft">Aug.8th Monday</td>
		<td>
		<table id="intable" width="100%" border="0" cellspacing="0"
			cellpadding="1">
			<tr>
			<td width="191">• The gel results of 5 backbones are right.</td>
			<td width="249">• Miniprep: pSB1C3, vgb+22M+10I</td>
			<td width="157">• Culture vgb+22M+1oI in hypoxia<br />
			•PCR pSB1C3</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.9th Tuesday</td>
		<td>
		<table id="intable" width="100%" border="0" cellspacing="0"
			cellpadding="1">
			<tr>
			<td width="33%">• Run the PCR product</td>
			<td width="33%">• PCR pSB1C3 again</td>
			<td width="33%">• Run the product, results are good.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.10th Wednesday</td>
		<td>
		<table width="100%" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="170">• Culture: 20H, 20J<br />
				• Transform 13K from plate 3</td>
				<td width="184">• Miniprep: 20H-1, 20J-1</td>
				<td>• Cut: the 20H-1, 20J-1, 22B-1, 22B-3 with E+P</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.11th Thursday</td>
		<td>
		<table width="100%" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Run the digestion results. Bands are confirmed right.</td>
				<td>• Colony PCR vgb+22M+10I</td>
				<td>• Cut the plasmid of vgb+22M+10I</td>


			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.12th Friday</td>
		<td>
		<table width="100%" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Make new stock of competent cells</td>
				<td>• Ligation: 13K+10I<br />
				• Cut the PCR results and 22M with E+P</td>
				<td>• Sequence: nirB, vgbL, 12I, 20H, 20J, 22B</td>
				<td>• Transform 13K+10I+pSB1K3<br />
				• Cut 13K to validate. Results are right.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.13th Saturday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Colony PCR: 13K+10I+pSB1K3</td>
				<td>• Culture: vgb+22M+10I in 5ml(shaking), 5ml(water bath),
				10ml(water bath), 15(water bath).</td>
				<td>• Check the YFP expression of 5ml(shaking) and 15ml(water
				bath). No yellow fluorescent cells,</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.14th Sunday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="244">• Transform: the Gibson assembly results.</td>
				<td width="164">• Miniprep: 13K+10I<br />
				• Cut: 13K+10I</td>
				<td>• Purification: the digestion results.<br />
				• Ligation: nirB+13K+10I</td>
			</tr>
		</table>
		</td>
	</tr>

</table>

<h1>Week7</h1>

<table id="notesheet" width="696" border="1" cellspacing="1"
	cellpadding="1">
	<tr>
		<td width="63">Day</td>
		<td width="621">Note</td>
	</tr>

	<tr>
		<td id="sheetleft">Aug.15th Monday</td>
		<td>
		<table id="intable" width="603" border="0" cellspacing="1"
			cellpadding="1">
			<tr>
			<td width="191">• Plate: nirB+13K+10I</td>
			<td width="249">• Colony PCR: vgb+YFP+tetR +terminater</td>
			<td width="157">• Gibson PCR</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.16th Tuesday</td>
		<td>
		<table id="intable" width="615" border="0" cellspacing="1"
			cellpadding="1">
			<tr>
			<td width="140">• Colony PCR: vgb+22M+10I, nirB+13K+10I</td>
			<td width="181">• No bands of 13K; 22M confirmed</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.17th Wednesday</td>
		<td>
		<table width="609" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="304">• Miniprep: 22M<br />
				• Cut: 22M</td>
				<td width="298">• Check CFP expression. No fluorescence.</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.18th Thursday</td>
		<td>
		<table width="618" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td>• Transform: 13K, 10I, 22M, 12I, 18P</td>



			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.19th Friday</td>
		<td>
		<table width="609" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="277">• Miniprep: 13K, 10I, 22M, 12I, 18P</td>
				<td width="227">• Cut: 13K, 10I, 22M, 12I, 18P</td>
				<td width="95">• Run the gel</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.20th Saturday</td>
		<td>
		<table width="620" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td>• Ligate 13K+10I, 22M+10I</td>


			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.21st Sunday</td>
		<td>
		<table width="620" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="244">• Transform: the Gibson assembly results.</td>
				<td width="164">• Miniprep: 13K+10I<br />
				• Cut: 13K+10I</td>
				<td>• Purification: the digestion results.<br />
				• Ligation: nirB+13K+10I</td>
			</tr>
		</table>
		</td>
	</tr>

</table>

<h1>Week8</h1>
<table id="notesheet" width="697" border="1" cellspacing="1"
	cellpadding="1">
	<tr>
		<td width="63">Day</td>
		<td width="620">Note</td>
	</tr>

	<tr>
		<td id="sheetleft">Aug. 22nd Monday</td>
		<td>
		<table id="intable" width="603" border="0" cellspacing="1"
			cellpadding="1">
			<tr>
			<td width="191">• Transform 13K+10I, 22M+10I</td>
			<td width="249">• Test new primers.<br />
			• PCR: 22M+10I, 13K+10I</td>
			<td width="157">• Run the PCR products.<br />
			• Cut the PCR products.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug. 23rd Tuesday</td>
		<td>
		<table id="intable" width="605" border="0" cellspacing="1"
			cellpadding="1">
			<tr>
			<td width="140">• Test primers: CS/CP, VF/VR, pSB1_f/r</td>
			<td width="181">• Cut: 11P, 1F, 22M<br />
			• Run the cut results.1F-1/2/3 are right.</td>
			<td width="126">• Mix the 1F-1/2 purification products</td>
			<td width="145">• Cut: 1F-1+1F-2(E+S), 22M-3(X+P), pSB1C3(E+P)</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug. 24th Wednesday</td>
		<td>
		<table width="620" border="0" cellspacing="1" cellpadding="1">
			<tr>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug. 25th Thursday</td>
		<td>
		<table width="618" border="0" cellspacing="1" cellpadding="1">
			<tr>




			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug. 26th Friday</td>
		<td>
		<table width="594" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="590">• Amplify: vgb, 1C3</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.27th Saturday</td>
		<td>
		<table width="606" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="602">• Digest: Vgb, 1C3, fdfhF, 22M+10I, 13K+10I</td>


			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Aug.28th Sunday</td>
		<td>
		<table width="608" border="0" cellspacing="1" cellpadding="1">
			<tr>
				<td width="366">• Ligate: vgb+22M+10I, fdfhF+13K+10I</td>
				<td width="235">• Transform the ligation results.</td>

			</tr>
		</table>
		</td>
	</tr>

</table>
<br />
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<h1>Biofilm Group</h1>
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<p style="clear: both;"></p>
<div id="page2">
<div class="block" id="nsheet">
<h1>1st August</h1>

<p>Freeze slicing of about 50μm. Observe under natural light
microscope and can see red florescence. The thickness is about 130μm</p>
</div>
<div class="block" id="nsheet">
<h1>4th August</h1>
<p>Repeat the last experiment with silicone tube. 6rpm/s results in
a flowing speed of 68ml/day</p>
</div>
<div class="block" id="nsheet">
<h1>6th August</h1>
<p>Similar to the last time. Did not use freeze slicing.</p>
</div>
<div class="block" id="nsheet">
<h1>15th August</h1>
<p>Cultured E.coli in 5ml LB for 12h.</p>
</div>
<div class="block" id="nsheet">
<h1>16th August</h1>
<p>Substituting a part of silicone tube with glass tube in silicone
tube biofilm formation sets. Culture in 37℃</p>
</div>
<div class="block" id="nsheet">
<h1>17th August</h1>
<p>Add 50ml LB and culture with circular culture.</p>
</div>
<div class="block" id="nsheet">
<h1>18th August</h1>
<p>12.00 found one free-flow pump stopped. Cooled for 15 minutes and
turned on again. Could be over heated. Can see some bacteria on the
bottom of the vessel and tube. When the pump started again, the bacteria
was washed away.</p>
</div>
<div class="block" id="nsheet">
<h1>19th August</h1>
<p>Can observe obvious white biofilm where the silicone tube joins
the tube but cannot see red florescence, suspect contamination. No
biofilm is observed on the glass tube under microscope.</p>
</div>
<div class="block" id="nsheet">
<h1>21st, August</h1>
<p>Biofilm formation with large test tubes. Inoculate with 1%
e.coli. Rubber tubes are attached to air pump with filter between air
pump and the tube to prevent entrance of germs. Two sets use MSM
+glucose medium and two sets use LB.<br />
Retry with glass tube biofilm formation set.</p>
</div>
<div class="block" id="nsheet">
<h1>24th, August</h1>
<p>Terminate biofilm formation, the glass slide left in the drawer
to dry. Can see obvious rod like structure under 400 magnification.
(spheres in MSM+glucose culture) No red florescence is seen. Most of the
surface is covered by single layer cells but some part of it has thick
bump like structure.<br />
No biofilm observed on the glass tube.</p>
</div>

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document.getElementById('page1').style.display='none'
 document.getElementById('pgae2').style.display='block'}
</script>
<p style="clear: both"></p>
</div>
<!--framecontent-->

<div style="display: none" class="frame" id="rightnav">
<div class="bgcolors" id="round">
<p><a name="jumptop" id="bb">&nbsp; Biobrick Group&nbsp;</a>|<a
	id="bf">&nbsp;Biofilm Group &nbsp;</a></p>
</div>
<!--bgcolors--></div>
<!--rightnav--></div>
<!--blue-->
<div class="links"><a href="#top2">Top</a></div>
</div>
<!--frame--></div>
<!--rightcontainer-->
<p style="clear: both"></p>

</div>
<!--main-->
<div class="footer" id="footer"><a href="http://2011.igem.org/">
iGem 2011 Home Page</a> <a href="http://ung.igem.org/Special:Upload/">
Upload Files</a> <a
	href="http://2011.igem.org/wiki/index.php?title=Template:Zjucss_main&action=edit">Edit
CSS</a> <a href="http://ung.igem.org/Team_Wikis?year=2011"> Team Wikis</a> <a
	href="mailto:zjuigem@gmail.com?"><strong>Contact Us</strong></a></div>
</div>
<!--contentwrapper--></div>
</body>
</html>
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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